I would really love to know what happened to the Dwemer. They're comparable to the Mayans, in a sense. Revolutionary technology in their day and age, and then they just disappeared.
If it were my game, and I made a questline about them, I would either have it be like looking back in time as you walk through a certain ruin, and you see flashbacks of the civilization and it's downfall, or, I would have a last bastion of the Dwemer, one last stronghold that they inhabit, perhaps on the verge of takeover by the Falmer or whatever caused their near extinction, and you have to assist them drive back the invaders and help protect this last safe haven.
But, two Snow Elves will suffice for now, I suppose.
I expect some Dwemer storyline in an Elder Scrolls VI, Bethesda xD (and more than the aetherium crap in Dawnguard)